In this ongoing project, the use of harmonic analysis of large systems is used in a variety of ways to provide a better understanding of a protein and RNA systems. This work has involved performing many different types of harmonic analysis methods to the bovine pancreatic trypsin inhibitor as a trial system. Both harmonic and quasiharmonic analysis calculations have been carried out in several different basis. These results are currently being analyzed and written up. There has also been extensive analysis of the time behavior of the results from harmonic analysis and a direct comparison with simulation results. Further work involving the Langevin mode analysis of this trial system and other systems is planned. From this work we hope to: (1) better explain neutron spectral (time of flight) data, (2) better characterize friction and solvent damping, (3) find stress points in macromolecules, and (4) explain (or predict) some site specific mutation data.